Biopolym. Cell. 2001; 17(4):331-336.
Bioorganic Chemistry
Interacion of cyanine dyes with nucleic acids. 23. Computer simulation of «half-intercalative» interaction of monomethyne cyanine dyes with DNA
1Lukashov S. S., 2Kachkovsky G. O., 1Yarmoluk S. M., 1Matsuka G. Kh.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01033


Computer simulation of interaction with DNA of six monomethyne cyanine dyes was carried out using MM+, AMBER, PM3 and CNDO/2 methods from Hyperchem 5.0 program packet. Geometry optimization of complexes was carried out, charge density for ground S0 and exited 5] states and potential energies of heterocyeles' rotation around the bonds of methyne group for unbound dyes and dyes in complexes with DNA were calculated. Obtained energies of complexes are in agreement with observed fluorescent intensities of dyes in presence of DNA, Calculated electron density distribution changes in dyes' molecules upon DNA binding diverge with observed Stocks' shift values changes. Rotation potential energy values show that rigidity of fixation of dye's molecule planar conformation increases strongly upon binding to DNA.


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